Optimizing hierarchical protein design for nanotechnology

Optimizing hierarchical protein design for nanotechnology

Proteins and artificial protein-like polymers have long been of interest as nanotech engineering materials for building atomically precise nanosystems. Mechanical strength and robustness are highly desirable properties for such use, and some natural proteins—like keratin (horn) and silk—offer superior properties (see this post over at Eric Drexler’s blog Metamodern). New computational results reveal how the proper hierarchical assembly of smaller protein domains optimizes mechanical properties. From MIT, via AAAS EurekAlert “Simplicity is crucial to design optimization at nanoscale“, written by Denise Brehm:

MIT researchers who study the structure of protein-based materials with the aim of learning the key to their lightweight and robust strength have discovered that the particular arrangement of proteins that produces the sturdiest product is not the arrangement with the most built-in redundancy or the most complicated pattern. Instead, the optimal arrangement of proteins in the rope-like structures they studied is a repeated pattern of two stacks of four bundled alpha-helical proteins.

This composition of two repeated hierarchies (stacks and bundles) provides great strength—the ability to withstand mechanical pressure without giving way—and great robustness—the ability to perform mechanically, even if flawed. Because the alpha-helical protein serves as the building block of many common materials, understanding the properties of those materials has been the subject of intense scientific inquiry since the protein’s discovery in the 1940s.

In a paper published in the Jan. 27 online issue of Nanotechnology[abstract], Markus Buehler and Theodor Ackbarow describe a model of the protein’s performance, based on molecular dynamics simulations. With their model they tested the strength and robustness of four different combinations of eight alpha-helical proteins: a single stack of eight proteins, two stacks of four bundled proteins, four stacks of two bundled proteins, and double stacks of two bundled proteins. Their molecular models replicate realistic molecular behavior, including hydrogen bond formation in the coiled spring-like alpha-helical proteins.

“The traditional way of designing materials is to consider properties at the macro level, but a more efficient way of materials’ design is to play with the structural makeup at the nanoscale,” said Buehler, the Esther and Harold E. Assistant Professor in the Department of Civil and Environmental Engineering. “This provides a new paradigm in engineering that enables us to design a new class of materials.”

More and more frequently, natural protein materials are being used as inspiration for the design of synthetic materials that are based on nanowires and carbon nanotubes, which can be made to be much stronger than biological materials. Buehler and Ackbarow’s work demonstrates that by rearranging the same number of nanoscale elements into hierarchies, the performance of a material can be radically changed.

The insights from this work might aid in the design of novel materials using peptide and protein building blocks.—Jim